Molecular Characterization of Increased Amplicon Lengths in SARS-CoV-2 Reverse Transcription Loop-Mediated Isothermal Amplification Assays

Loop-mediated isothermal amplification (LAMP) is a power tool for the amplification of specific RNA and DNA targets. Much like PCR, LAMP requires primers that surround a target amplification region and generates exponential product through a unique highly specific daisy-chain single-temperature amplification reaction. However, until recently, attempts to amplify targets of greater than 200 base pairs (bp) have been mostly unsuccessful and limited to short amplicon targets of less than 150 bp. Although short amplicons have the benefit of a rapid detection (<40 min), they do not allow for the prediction of RNA integrity based on RNA length and possible intactness. In this study, 8 primer sets were developed using 2 LAMP primer-specific software packages against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid gene with insert lengths ranging from 262 to 945 bp in order to amplify and infer the integrity of viral RNA. Because these amplification lengths are greater than the current methods that use an insert length of 130 or less, they require a longer incubation, modified primer and temperature strategies, and the addition of specific adjuncts to prevent nonspecific amplification. This proof of concept study resulted in successful reverse transcription LAMP reactions for amplicon targets of 262, 687, 693, and 945 bp using a clinical nasopharyngeal NP sample, purified SARS-CoV-2 RNA, and crude lysate containing inactivated virus.

Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step

The ongoing COVID-19 pandemic has created an unprecedented need for rapid diagnostic testing. The World Health Organization (WHO) recommends a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 testing. The goal of this study was to determine whether SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether. The direct RT-qPCR approach correctly identified 92% of a reference set of blinded NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Importantly, the direct method had sufficient sensitivity to reliably detect those patients with viral loads that correlate with the presence of infectious virus. Thus, this strategy has the potential to ease supply choke points to substantially expand COVID-19 testing and screening capacity and should be applicable throughout the world.

DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP

The ongoing COVID-19 pandemic has caused an unprecedented need for rapid diagnostic testing. The Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) recommend a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 testing. We hypothesized that SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether, and tested this hypothesis on a series of blinded clinical samples. The direct RT-qPCR approach correctly identified 92% of NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Thus, direct RT-qPCR could be a front-line approach to identify the substantial majority of COVID-19 patients, reserving a repeat test with RNA extraction for those individuals with high suspicion of infection but an initial negative result. This strategy would drastically ease supply chokepoints of COVID-19 testing and should be applicable throughout the world.

Effective-medium theory of elastic waves in random networks of rods

We formulate an effective medium (mean field) theory of a material consisting of randomly distributed nodes connected by straight slender rods, hinged at the nodes. Defining wavelength-dependent effective elastic moduli, we calculate both the static moduli and the dispersion relations of ultrasonic longitudinal and transverse elastic waves. At finite wave vector k the waves are dispersive, with phase and group velocities decreasing with increasing wave vector. These results are directly applicable to networks with empty pore space. They also describe the solid matrix in two-component (Biot) theories of fluid-filled porous media. We suggest the possibility of low density materials with higher ratios of stiffness and strength to density than those of foams, aerogels, or trabecular bone.

[Thoracic and thoraco-lumbar discs herniations: diagnosis and therapeutic management]

Summary Management of symptomatic thoracic disc hemiations is difficult because of their polymorphic symptomatology and hardness to join the intervertebral thoracic disc surgically. The objective of this study was first to show the difficult diagnosis of these discal herniations and their posterior approach particularities; secondly, to analyse our results and compare them with those of the literature. This retrospective study analyses a four patients series operated between January 1997 and march 2003 using intraoperative somatosensory evoked potentials. All of them had before surgical management, a lumbar Xray or a MRI. The average postoperative follow-up was seven months. All patients were males with a mean age of 39.5 years old (extremes: 22-59). They had systematisation of their lumboradiculalgia, leading to an average delayed diagnosis of 10 months. The disc herniation was paramedian in three cases, median in one,. It was in T10-T11 in one case, in T11-T12 in two and in T12-L1 in one. All the patients were operated on with a posterior approach, recording the intraoperative somatosensory evoked potentials. Disc herniation was resected in three cases. Functional results were satisfactory (no pains for three patients) in the follow-up period of seven months. Every patient presenting with an atypical lumboradiculalgia must have a spine MRI to diagnose the symptomatic thoracic disc herniation. Surgery has good results if technical details are used respecting the threatened spinal cord.

Pharmacokinetics and hemostatic effects of saruplase in patients with acute myocardial infarction: comparison of infusion, single-bolus, and split-bolus administration

Saruplase, or unglycosylated, single-chain urokinase-type plasminogen activator (scu-PA) selectively activates fibrin-bound plasminogen, and is subsequently converted to its two-chain derivative tcu-PA (urokinase) by plasmin. The efficacy of a 20 mg IV bolus followed by an infusion of 60 mg over 1 hour (standard regimen) has been demonstrated in acute myocardial infarction (AMI). The Bolus Administration of Saruplase in Europe (BASE) study compared the efficacy of standard therapy, single bolus (80 mg), and split bolus (2 x 40 mg at 30-minute intervals) in AMI. In a substudy of BASE, the pharmacokinetics of total u-PA activity (amidolytic activity after plasmin treatment), high molecular weight (HMW) u-PA antigen, and tcu-PA activity were compared in patients receiving standard therapy (n = 4), single bolus (n = 4), or split bolus (n = 5). Total u-PA activity and HMW u-PA antigen were similar. The maximum concentration (C(max,), mean +/- SD) of total u-PA activity was 2.2 +/- 0.3 microg/mL after standard therapy, 16.3 +/- 3.9 microg/mL after single bolus, and 8.2 +/- 1.6 ug/mL after split bolus. The area under the concentration versus time curve (AUC) values of total u-PA activity were 1.7 +/- 0.1 microg/mL*h (standard therapy), 4.0 +/- 0.9 microg/mL*h (bolus), and 3.0 +/- 0.7 microg/mL*h (split bolus). The dominant initial half-lives (t(1/2) alpha) were 7.1 +/- 1.1 minutes (standard), 8.8 +/- 0.8 minutes (bolus), and 5.1 +/- 2.1 minutes (split bolus). Maximum plasma concentrations of of tcu-PA activity were observed at 5.2 +/- 7 minutes (standard), 21 +/- 10 minutes (bolus), and 42 +/- 2 minutes (split bolus). C(max) was lowest after standard therapy (0.6 +/- 0.3 microg/mL), highest after bolus (4.2 +/- 2.2 microg/mL), and approximately twice as high as standard therapy after split bolus (1. 3 +/- 0.8 microg/mL). After standard therapy the mean fibrinogen concentration decreased gradually from approximately 300 mg/dL to 70 mg/dL at 90 and 120 minutes. After a single bolus the fibrinogen concentration decreased below the limit of quantification within 30 minutes and remained there for at least 120 minutes. Directly after the second 40 mg dose of the split bolus, the fibrinogen levels had an accelerated and more pronounced decrease to approximately 65 mg/dL at 90 and 120 minutes. A single bolus results in very high early total u-PA activity, which accelerates the appearance of tcu-PA activity and fibrinogen consumption. The pharmacokinetics and hemostatic effects of the split-bolus regimen are more comparable with those of standard therapy.

Porter's generic strategies, discontinuous environments, and performance: a longitudinal study of changing strategies in the hospital industry

OBJECTIVE

Changes in generic strategies in response to discontinuous environments have been relatively ignored in the management literature. This study reports an examination of the relationships between Porter's (1980) generic strategies, discontinuous environments, and performance.

DATA SOURCES

Archival data for 1984 and 1988 were collected for 172 acute care hospitals in Florida in order to test these relationships.

STUDY DESIGN

To examine fully the performance impact of changes in strategy in a discontinuous environment, a longitudinal research design that identified a firm's strategy at two points in time, 1984 and 1988, was used.

PRINCIPAL FINDINGS

Results indicate that firms with a proper strategy environment fit performed the highest, firms that did not change their strategy had no change in performance, and firms that changed their strategy toward a proper strategy environment showed an increase in performance.

CONCLUSION

Findings support the notion that hospitals with appropriate strategy-environment combinations will exhibit higher performance.

Cardiopulmonary effects of direct venous CO2 insufflation in ewes. A model for CO2 hysteroscopy

In order to mimic the delivery of CO2 into the pelvic circulation during sustained hysteroscopic surgery, direct insufflation of CO2 was done into the femoral vein of six anesthetized ewes. Following the establishment of baseline values in each animal, cardiac output, pulmonary arterial pressure (Ppa), pulmonary arterial wedge pressure (Ppw), arterial pH and gas levels, and ECG changes were recorded at ten-minute intervals. CO2 was delivered into the femoral circulation for 30 minutes. Following the experiment, measurements were repeated during a 20-minute recovery period. Ppa and Ppw increased significantly during the experiment but returned to baseline values after 70 minutes. Cardiac output, which increased significantly, remained high after the same period and was paralleled by cardiac rate. There was no significant change in systemic blood pressure or arterial oxygenation. Only at the highest flow rate were there observable changes in PCO2, accompanied by mild acidosis. One of the six animals displayed premature ventricular contractions at the inception of the highest flow rate. Since the delivery rate of CO2 per kilogram of body weight clearly exceeded that generally used in human hysteroscopic surgery (35-100 mL/min), these experimental results suggest that CO2, when employed as a distension modality in hysteroscopic surgery, displays a wide margin of safety.

A cluster analysis of Million Clinical Multiaxial Inventory (MCMI) profiles: more about a taxonomy of alcoholic subtypes

MCMI and MMPI data were obtained from 125 male veteran alcoholic inpatients. MCMI profiles were classified into five relatively homogeneous subgroups by a hierarchical clustering technique. One-way ANOVAs were calculated for each of the MMPI scales; patients were classified according to MCMI group membership. Results showed that conceptually meaningful clusters exist among MCMI profiles, that statistically significant relationships exist between MCMI profiles and MMPI scale scores, and that these relationships are consistent with trends reported in the literature. The study provides additional support for the idea that a potentially useful taxonomy exists for alcoholics and suggests that the MCMI could be a useful tool in subsequent research on understanding and treating different patterns of alcoholism.

Ego identity status, conformity behavior, and personality in late adolescence

Three related studies were completed to test the predictive relation among identity status, personality, and conformity behavior. The investigations were undertaken to replicate the earlier research findings of Toder and Marcia (1973). As predicted in Study 1, personality differences were found for both sexes. However, no relation was observed between identity status and conformity on the Asch task. Study 2 was completed to confirm the reliability of the identity status measure. Finally, in Study 3 four measures of conformity behavior (peer assessments, an experimental task, two self-report scales) were completed by college students of diffusion, foreclosure, moratorium, and identity-achievement statuses. Diffusion students were most influenced by peer pressure conformity, whereas identity-achievement students were most likely to report engaging in conformity behavior for achievement gains. Although earlier research by Toder and Marcia (1973) was not replicated via the Asch conformity task, the third study does support a predicted relation between identity and conformity behavior.

Ego identity status, conformity behavior, and personality in late adolescence

Three related studies were completed to test the predictive relation among identity status, personality, and conformity behavior. The investigations were undertaken to replicate the earlier research findings of Toder and Marcia (1973). As predicted in Study 1, personality differences were found for both sexes. However, no relation was observed between identity status and conformity on the Asch task. Study 2 was completed to confirm the reliability of the identity status measure. Finally, in Study 3 four measures of conformity behavior (peer assessments, an experimental task, two self-report scales) were completed by college students of diffusion, foreclosure, moratorium, and identity-achievement statuses. Diffusion students were most influenced by peer pressure conformity, whereas identity-achievement students were most likely to report engaging in conformity behavior for achievement gains. Although earlier research by Toder and Marcia (1973) was not replicated via the Asch conformity task, the third study does support a predicted relation between identity and conformity behavior.

Pregnancy following segmental isthmic reversal of the rabbit oviduct

Microsurgical reversal of a segment of rabbit proximal tubal isthmus has been followed by normal pregnency in the first two animals to undergo the procedure. Establishment of pregnancy despite radical modification of the oviduct furnishes the opportunity to gain new insights into the mechanisms controlling tubal ovum transport and emphasizes the evolving feasibility and importance of tuboplastic microsurgery both as a research tool and clinical procedure.